Structured Intelligence

A repository for production-ready AI assets that improve coding, research, and writing throughput.

Repository: https://github.com/Scientific-Tooling/structured-intelligence

License: MIT, see LICENSE

What Lives Here

• agents/: Task-specific agents with prompts, config, and smoke tests.
• skills/: Reusable capabilities packaged with config.yaml, SKILL.md, scripts, references, and assets.
• workflows/: End-to-end operating playbooks for coding, research, and writing.
• knowledge/: Reusable source material, notes, and generated outputs.
• prompts/: Shared persona and task prompt libraries.
• scripts/: Local automation for scaffolding and validation.
• docs/: Architecture and contribution conventions.

Availability

This repository is publicly available at https://github.com/Scientific-Tooling/structured-intelligence. It contains reusable local skills, agents, workflows, validation scripts, and manuscript-style documentation for selected skills. The repository is intended for local use in AI-assisted coding and research environments that support filesystem-discovered skill bundles.

Relevant project-site, manuscript, and skill materials include:

• docs/index.html
• docs/ncbi-eutilities-assistant-manuscript.md
• docs/rpsblast-assistant-manuscript.md
• manuscripts/
• skills/ncbi-eutilities-assistant/
• skills/rpsblast-assistant/

The repository also includes a lightweight project landing page at docs/index.html and manuscript web pages under manuscripts/, suitable for project-scoped GitHub Pages hosting at https://scientifictooling.org/structured-intelligence/.

Quick Start

Use The research Skill

After cloning this repository:

# Default target: Codex (~/.codex/skills)
./scripts/install_skill.sh research

# Claude Code (~/.claude/skills)
./scripts/install_skill.sh research --tool claude

# Other tools (custom skills directory)
./scripts/install_skill.sh research --dest ~/.my-tool/skills

Then restart your tool session and ask for research.

Use The rpsblast-assistant Skill

Install the skill:

# Default target: Codex (~/.codex/skills)
./scripts/install_skill.sh rpsblast-assistant

# Claude Code (~/.claude/skills)
./scripts/install_skill.sh rpsblast-assistant --tool claude

Then restart your tool session and use natural language.

Codex examples:

Use $rpsblast-assistant to tell me what I need to download for a local RPS-BLAST workflow.

Use $rpsblast-assistant to download the minimal CDD database and rpsbproc annotation files into ./db and ./data.

Use $rpsblast-assistant to check whether my local setup is complete for running rpsblast with db/Cdd.

Use $rpsblast-assistant to run rpsblast on ./sequence.fasta against ./db/Cdd with E-value 0.01 and then post-process with rpsbproc.

Use $rpsblast-assistant to explain the format of sequence.out and tell me which part is the real tabular data.

Claude Code examples:

Use rpsblast-assistant to tell me what I need to download for a local RPS-BLAST workflow.

Use rpsblast-assistant to download the minimal CDD database and rpsbproc annotation files into ./db and ./data.

Use rpsblast-assistant to check whether my local setup is complete for running rpsblast with db/Cdd.

Use rpsblast-assistant to run rpsblast on ./sequence.fasta against ./db/Cdd with E-value 0.01 and then post-process with rpsbproc.

Use rpsblast-assistant to explain the format of sequence.out and tell me which part is the real tabular data.

Use The ncbi-eutilities-assistant Skill

Install the skill:

# Default target: Codex (~/.codex/skills)
./scripts/install_skill.sh ncbi-eutilities-assistant

# Claude Code (~/.claude/skills)
./scripts/install_skill.sh ncbi-eutilities-assistant --tool claude

Then restart your tool session and use natural language.

Codex examples:

Use $ncbi-eutilities-assistant to search PubMed for "CRISPR base editing" and show me the exact E-utilities request first.

Use $ncbi-eutilities-assistant to run a PubMed workflow for "single-cell foundation model" and save the results under ./pubmed-run.

Use $ncbi-eutilities-assistant to run a PubMed review workflow for "large language model systematic review" over the last 365 days and extract structured abstracts into ./pubmed-review.

Use $ncbi-eutilities-assistant to show me the last 7 days of CRISPR progress on PubMed and write a concise update brief under ./crispr-weekly-brief.

Use $ncbi-eutilities-assistant to summarize the last 30 days of base editing research on PubMed into a markdown update brief.

Use $ncbi-eutilities-assistant to fetch PubMed summaries for PMID 39696283 and 39650267 as JSON.

Claude Code examples:

Use ncbi-eutilities-assistant to search PubMed for "CRISPR base editing" and show me the exact E-utilities request first.

Use ncbi-eutilities-assistant to run a PubMed workflow for "single-cell foundation model" and save the results under ./pubmed-run.

Use ncbi-eutilities-assistant to run a PubMed review workflow for "large language model systematic review" over the last 365 days and extract structured abstracts into ./pubmed-review.

Use ncbi-eutilities-assistant to show me the last 7 days of CRISPR progress on PubMed and write a concise update brief under ./crispr-weekly-brief.

Use ncbi-eutilities-assistant to summarize the last 30 days of base editing research on PubMed into a markdown update brief.

Use ncbi-eutilities-assistant to fetch PubMed summaries for PMID 39696283 and 39650267 as JSON.

Build This Repository

1. Add an agent from agents/_templates/agent.
2. Add a skill from skills/_templates/skill.
3. Register both in their registry.yaml files.
4. Follow the relevant workflow under workflows/.
5. Run ./scripts/validate_structure.sh before commit. It checks the required top-level structure plus registry/schema rules for registered assets.
6. Run ./scripts/sync_site_theme.sh after updating shared page typography in the Scientific-Tooling.github.io repository. It syncs the shared theme.css into docs/ and manuscripts/ so project pages keep the same hero-title and typography system as the organization homepage.

Shared Page Theme

Use this workflow whenever you add a new public-facing page or change hero-title styles:

1. Treat Scientific-Tooling.github.io/theme.css as the source of truth for shared typography tokens and semantic title classes.
2. If you change shared title styling there, run ./scripts/sync_site_theme.sh in this repository before editing downstream pages.
3. In every new page, include the shared theme before the page stylesheet:
   • project pages: ./theme.css then ./site.css
   • manuscript pages: ./theme.css or ../theme.css then the local stylesheet
4. Use semantic classes instead of redefining hero sizes per page:
   • .title-hero
   • .title-hero--wide
   • .title-section
   • .lede
   • .eyebrow
5. Keep page-specific CSS focused on layout and spacing. Do not redefine shared hero-title font sizes or families in page-level styles unless you are changing the shared system itself.

Citation And Reuse

If you reference this repository in scientific writing, cite the repository URL and the access date, and identify the relevant manuscript or skill directory when possible. For example, the skill-focused manuscripts in docs/ describe the corresponding implementations under skills/.

Independence And Upstream Rights

This repository provides independent, unofficial AI interaction layers around existing scientific tools, APIs, and workflows. It does not claim ownership of the underlying third-party software, databases, services, or documentation, and it does not imply endorsement by the original authors, maintainers, or institutions.

The intent is to add a transparent interface layer for local AI-assisted use, not to reproduce or replace the original applications. Users remain responsible for complying with the licenses, terms of use, attribution requirements, and usage policies of the upstream tools and data sources they invoke through these skills.

License

This repository is distributed under the MIT License. See LICENSE.